+++ /dev/null
-package fr.orsay.lri.varna.models.annotations;
-
-import java.awt.Color;
-import java.awt.geom.Point2D;
-import java.io.Serializable;
-
-import javax.xml.transform.sax.TransformerHandler;
-
-import org.xml.sax.SAXException;
-import org.xml.sax.helpers.AttributesImpl;
-
-import fr.orsay.lri.varna.models.rna.ModeleBase;
-import fr.orsay.lri.varna.utils.XMLUtils;
-
-
-public class ChemProbAnnotation implements Serializable {
-
- public static final String HEADER_TEXT = "ChemProbAnnotation";
-
- /**
- *
- */
- private static final long serialVersionUID = 5833315460145031242L;
-
-
- public enum ChemProbAnnotationType
- {
- TRIANGLE,
- ARROW,
- PIN,
- DOT;
- };
-
- public static double DEFAULT_INTENSITY = 1.0;
- public static ChemProbAnnotationType DEFAULT_TYPE = ChemProbAnnotationType.ARROW;
- public static Color DEFAULT_COLOR = Color.blue.darker();
-
- private ModeleBase _mbfst;
- private ModeleBase _mbsnd;
- private Color _color;
- private double _intensity;
- private ChemProbAnnotationType _type;
- private boolean _outward;
-
- public static String XML_ELEMENT_NAME = "ChemProbAnnotation";
- public static String XML_VAR_INDEX5_NAME = "Index5";
- public static String XML_VAR_INDEX3_NAME = "Index3";
- public static String XML_VAR_COLOR_NAME = "Color";
- public static String XML_VAR_INTENSITY_NAME = "Intensity";
- public static String XML_VAR_TYPE_NAME = "Type";
- public static String XML_VAR_OUTWARD_NAME = "Outward";
-
- public void toXML(TransformerHandler hd) throws SAXException
- {
- AttributesImpl atts = new AttributesImpl();
- atts.addAttribute("","",XML_VAR_INDEX5_NAME,"CDATA",""+_mbfst.getIndex());
- atts.addAttribute("","",XML_VAR_INDEX3_NAME,"CDATA",""+_mbsnd.getIndex());
- atts.addAttribute("","",XML_VAR_COLOR_NAME,"CDATA",XMLUtils.toHTMLNotation(_color));
- atts.addAttribute("","",XML_VAR_INTENSITY_NAME,"CDATA",""+_intensity);
- atts.addAttribute("","",XML_VAR_TYPE_NAME,"CDATA",""+_type);
- atts.addAttribute("","",XML_VAR_OUTWARD_NAME,"CDATA",""+_outward);
- hd.startElement("","",XML_ELEMENT_NAME,atts);
- hd.endElement("","",XML_ELEMENT_NAME);
- }
-
-
- public ChemProbAnnotation(ModeleBase mbfst, ModeleBase mbsnd, String styleDesc) {
- this(mbfst,mbsnd);
- applyStyle(styleDesc);
- }
-
- public ChemProbAnnotation(ModeleBase mbfst, ModeleBase mbsnd) {
- this(mbfst,mbsnd,ChemProbAnnotation.DEFAULT_TYPE,ChemProbAnnotation.DEFAULT_INTENSITY);
- }
-
- public ChemProbAnnotation(ModeleBase mbfst, ModeleBase mbsnd, double intensity) {
- this(mbfst,mbsnd,ChemProbAnnotation.DEFAULT_TYPE,intensity);
- }
-
- public ChemProbAnnotation(ModeleBase mbfst, ModeleBase mbsnd, ChemProbAnnotationType type) {
- this(mbfst,mbsnd,type,ChemProbAnnotation.DEFAULT_INTENSITY);
- }
-
- public ChemProbAnnotation(ModeleBase mbfst, ModeleBase mbsnd, ChemProbAnnotationType type, double intensity) {
- this(mbfst,mbsnd, type, intensity, DEFAULT_COLOR, true);
- }
-
- public ChemProbAnnotation(ModeleBase mbfst, ModeleBase mbsnd, ChemProbAnnotationType type, double intensity, Color color, boolean out) {
- if (mbfst.getIndex()>mbsnd.getIndex())
- {
- ModeleBase tmp = mbsnd;
- mbsnd = mbfst;
- mbfst = tmp;
- }
- _mbfst = mbfst;
- _mbsnd = mbsnd;
- _type = type;
- _intensity = intensity;
- _color = color;
- _outward = out;
- }
-
- public boolean isOut()
- {
- return _outward;
- }
-
- public void setOut(boolean b)
- {
- _outward = b;
- }
-
- public Color getColor()
- {
- return _color;
- }
-
- public double getIntensity()
- {
- return _intensity;
- }
-
- public ChemProbAnnotationType getType()
- {
- return _type;
- }
-
- public void setColor(Color c){
- _color = c;
- }
-
- public void setIntensity(double d){
- _intensity = d;
- }
-
- public Point2D.Double getAnchorPosition()
- {
- Point2D.Double result = new Point2D.Double(
- (_mbfst.getCoords().x+_mbsnd.getCoords().x)/2.0,
- (_mbfst.getCoords().y+_mbsnd.getCoords().y)/2.0);
- return result;
- }
-
- public Point2D.Double getDirVector()
- {
- Point2D.Double norm = getNormalVector();
- Point2D.Double result = new Point2D.Double(-norm.y,norm.x);
- Point2D.Double anchor = getAnchorPosition();
- Point2D.Double center = new Point2D.Double(
- (_mbfst.getCenter().x+_mbsnd.getCenter().x)/2.0,
- (_mbfst.getCenter().y+_mbsnd.getCenter().y)/2.0);
- Point2D.Double vradius = new Point2D.Double(
- (center.x-anchor.x)/2.0,
- (center.y-anchor.y)/2.0);
- if (_outward)
- {
- if (result.x*vradius.x+result.y*vradius.y>0)
- {
- return new Point2D.Double(-result.x,-result.y);
- }
- }
- else
- {
- if (result.x*vradius.x+result.y*vradius.y<0)
- {
- return new Point2D.Double(-result.x,-result.y);
- }
- }
- return result;
- }
- public Point2D.Double getNormalVector()
- {
- Point2D.Double tmp;
- if (_mbfst==_mbsnd)
- {
- tmp = new Point2D.Double(
- (-(_mbsnd.getCenter().y-_mbsnd.getCoords().y)),
- ((_mbsnd.getCenter().x-_mbsnd.getCoords().x)));
- }
- else
- {
- tmp = new Point2D.Double(
- (_mbsnd.getCoords().x-_mbfst.getCoords().x)/2.0,
- (_mbsnd.getCoords().y-_mbfst.getCoords().y)/2.0);
- }
-
- double norm = tmp.distance(0, 0);
- Point2D.Double result = new Point2D.Double(tmp.x/norm,tmp.y/norm);
- return result;
- }
-
- public static ChemProbAnnotationType annotTypeFromString(String value)
- {
- if (value.toLowerCase().equals("arrow"))
- {return ChemProbAnnotationType.ARROW;}
- else if (value.toLowerCase().equals("triangle"))
- {return ChemProbAnnotationType.TRIANGLE;}
- else if (value.toLowerCase().equals("pin"))
- {return ChemProbAnnotationType.PIN;}
- else if (value.toLowerCase().equals("dot"))
- {return ChemProbAnnotationType.DOT;}
- else
- {return ChemProbAnnotationType.ARROW;}
- }
-
-
- public void applyStyle(String styleDesc)
- {
- String[] chemProbs = styleDesc.split(",");
- for (int i = 0; i < chemProbs.length; i++) {
- String thisStyle = chemProbs[i];
- String[] data = thisStyle.split("=");
- if (data.length==2)
- {
- String name = data[0];
- String value = data[1];
- if (name.toLowerCase().equals("color"))
- {
- Color c = Color.decode(value);
- if (c==null)
- { c = _color; }
- setColor(c);
- }
- else if (name.toLowerCase().equals("intensity"))
- {
- _intensity = Double.parseDouble(value);
- }
- else if (name.toLowerCase().equals("dir"))
- {
- _outward = value.toLowerCase().equals("out");
- }
- else if (name.toLowerCase().equals("glyph"))
- {
- _type= annotTypeFromString(value);
- }
- }
- }
- }
-
- public void setType(ChemProbAnnotationType s)
- {
- _type = s;
- }
-
- public ChemProbAnnotation clone()
- {
- ChemProbAnnotation result = new ChemProbAnnotation(this._mbfst,this._mbsnd);
- result._intensity = _intensity;
- result._type = _type;
- result._color= _color;
- result._outward = _outward;
- return result;
- }
-
- public String toString()
- {
- return "Chem. prob. "+this._type+" Base#"+this._mbfst.getBaseNumber()+"-"+this._mbsnd.getBaseNumber();
- }
-
-}
git://source.jalview.org / jalview.git / blobdiff